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Cis-regulatory Sequences02:02

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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Flow-sorting and Exome Sequencing of the Reed-Sternberg Cells of Classical Hodgkin Lymphoma
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Whole exome sequencing in the rat.

Julie F Foley1, Dhiral P Phadke2, Owen Hardy3

  • 1Biomolecular Screening Branch, National Institute of Environmental Health Sciences, 111 T.W. Alexander Dr. Research Triangle Park, Durham, NC, USA. foley1@niehs.nih.gov.

BMC Genomics
|June 22, 2018
PubMed
Summary

Researchers developed a novel probe set for whole exome sequencing (WES) in rats. This tool accurately detects genetic variants in cancer-related genes, advancing translational research.

Keywords:
C6COSMICDSL-6A/C1FAT7NBTIINext generation sequencingSangerWhole exome sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • The rat genome's 2004 sequencing aimed to enhance human health via gene discovery and animal models.
  • Whole exome sequencing (WES) is crucial for identifying genetic variants.
  • Rat models are vital for understanding human diseases and environmental impacts.

Purpose of the Study:

  • To develop and validate a probe set for rat whole exome sequencing (WES).
  • To detect sequence variants in rat exons and untranslated regions (UTRs).
  • To compare mutations in cancer-related genes with human databases for translational research.

Main Methods:

  • In-silico probe design targeting the rat exome (RGSC6.0/rn6 RefSeq, Ensembl transcripts).
  • Whole exome sequencing (WES) of chemically induced rat tumor cell lines and normal rat liver tissue (FF and FFPE).
  • Bioinformatic analysis and Sanger validation of identified variants, including comparison with the Catalogue of Somatic Mutations in Cancer (COSMIC) database.

Main Results:

  • Designed 826,878 unique probe sequences, with 94.2% aligning to the rat genome.
  • Achieved coverage of 25,249 genes (95.8%) by at least one probe and 23,603 genes (93.5%) with full exon coverage.
  • Demonstrated high performance metrics for WES and validated cancer gene mutations, identifying exonic variants in cancer-related genes.

Conclusions:

  • An in-silico designed probe set effectively enriches the rat exome for DNA sequencing.
  • The WES platform shows high sensitivity and specificity for detecting variants, including potential chemically induced somatic mutations.
  • This genomic discovery tool aids in identifying rat genomic variants relevant to disease etiology and human translational research.